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HWxtest (version 1.0.5)

mtest: Performs an exact test using Monte Carlo trials for Hardy-Weinberg proportions

Description

Given a set of genotype counts, mtest examines a large number of possible outcomes with the same set of allele counts. For each table, it computes four test statistics and compares them with the observed values. It returns the total probability of all tables with test statistics as extreme or more so than the observed. It can also plot a histogram of one of the statitistics if histobins is greater than zero. More about these four test statistics and other information can be found in the vignette. This function will not usually be called directly by the user. Instead, call hwx.test with method set to either auto or monte.

Usage

mtest(c, ntrials = 1e+05, statName = "LLR", histobins = 0,
  histobounds = c(0, 0), showCurve = T, safeSecs = 100, detail = 2)

Arguments

c
A matrix containing the genotype counts. It should be a square matrix, but only the lower-left half is used.
ntrials
the number of random trials to perform
statName
can be LLR, Prob, U, or Chisq depending on which one is to be ploted. Note that P values for all four are computed regardless of which one is specified with this parameter.
histobins
If 0 no histogram is plotted. If 1 or TRUE a histogram with 500 bins is plotted. If set to a number greater than 1, a histogram with histobins is plotted.
histobounds
A vector containing the left and right boundaries for the histogram's x axis. If you leave this as the default, c(0,0), then mtest will compute reasonable bounds to include most of the distribution.
showCurve
whether to show a blue curve indicating the asymptotic (chi squared) distribution. This only works for LLR and Chisq
safeSecs
After this many seconds the calculation will be aborted. This is a safety valve to prevent attempts to compute impossibly large sets of tables.
detail
Determines how much detail is printed. If it is set to 0, nothing is printed (useful if you use mtest programmatically.).

Value

  • mtest returns a list components
  • $ PvaluesThe four computed P values corresponding to the test statistics: LLR, Prob, U and Chisq in that order.
  • $ seStandard errors for the P values. These come from the binomial.
  • $ observedThe four observed statistics in the same order as above
  • $ ntrialsThe number of tables examined during the calculation
  • $ genotypesThe input matrix of genotype counts
  • $ allelesThe allele counts $m$ corresponding to the input genotype counts

References

The methods are described by http://dx.doi.org/10.1534/genetics.109.108977{Engels, 2009. Genetics 183:1431}.

See Also

hwx.test